getMeanQualityProfile: Get quality profile of a fastq file(s).

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

Description

This function generates a table that reports the mean quality scores observed at each sequence position for the input fastq file(s).

Usage

getMeanQualityProfile(fl, n = 5e+05, project, layout = "Single")

Arguments

fl	(Required). character. File path(s) to fastq or fastq.gz file(s).
n	(Required). Default 500,000. The number of records to sample from the fastq file.
project	(Required). Provide a character label that describes the data being handled.
layout	(Required). Default is Single. Provide "Single" if handling single-end data; "Forward" if handling foward-reads, and "Reverse" if handling reverse-reads.

Details

Code modified from DADA2's plotQualityProfile function

Value

A table with the following column names: c("Position", "Mean", "Orientation", "Study")

ananata/fastq2otu documentation built on Feb. 2, 2022, 4:20 p.m.